How to Save Sverchok nodes
Something similar happens with Materials/node trees that are not used by any objects (ie - don't have "users". Objects produced by Sverchok don't automatically make those objects a user of a Sverchok node tree. You might need to press the "F" icon in the nodetree header toolbar (or Shield icon in 2.8+), to add a fake user to the node tree, then save.

The issue is Old. We discuss this on the Sverchok issue tracker back in 2014 - https://github.com/nortikin/sverchok/issues/356 )